Understanding temporal and spatial distribution of canopy transpiration is indispensable in hydrology and hydroecology. Canopy transpiration in a karst basin is controlled by meteorological conditions, plant species, and water in soil and rock fractures. Estimation of canopy transpiration at catchment scale in such heterogeneously hydrogeological conditions is challenging. Hydrological modeling is a useful method to estimate canopy transpiration at catchment scale, and it can be used to evaluate the effect of land-cover change. In this study, a distributed hydrological model was used to estimate canopy transpiration within a small karst watershed for the period July 28, 2007, to October 19, 2007. The results show that transpiration was about 19.2 percent of total rainfall, and daily transpiration rate in this basin ranged from 0.01 to 3.4 mm/day with an average of 0.8 mm/day during the study period. Epikarst water is an important water source for canopy transpiration in addition to soil water in the karst basin. And land-cover change has important effects on canopy transpiration in this area.